Selective recognition of metal ions by metalloregulatory proteins

The effect of dietary zinc and zinc physiological status on the composition of the gut microbiome in vivo

Zinc serves critical catalytic, regulatory, and structural roles. Hosts and their resident gut microbiota both require zinc, leading to competition, where a balance must be maintained. This systematic review examined evidence on dietary zinc and physiological status (zinc deficiency or high zinc/zinc overload) effects on gut microbiota. This review was conducted according to PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines and registered in PROSPERO (CRD42021250566). PubMed, Web of Science, and Scopus databases were searched for in vivo (animal) studies, resulting in eight selected studies. Study quality limitations were evaluated using the SYRCLE risk of bias tool and according to ARRIVE guidelines. The results demonstrated that zinc deficiency led to inconsistent changes in α-diversity and short-chain fatty acid production but led to alterations in bacterial taxa with functions in carbohydrate metabolism, glycan metabolism, and intestinal mucin degradation. High dietary zinc/zinc overload generally resulted in either unchanged or decreased α-diversity, decreased short-chain fatty acid production, and increased bacterial metal resistance and antibiotic resistance genes. Additional studies in human and animal models are needed to further understand zinc physiological status effects on the intestinal microbiome and clarify the applicability of utilizing the gut microbiome as a potential zinc status biomarker.

Arsenic pollution cycle, toxicity and sustainable remediation technologies: A comprehensive review and bibliometric analysis

Arsenic pollution and its allied impacts on health are widely reported and have gained global attention in the last few decades. Although the natural distribution of arsenic is limited, anthropogenic activities have increased its mobility to distant locations, thereby increasing the number of people affected by arsenic pollution. Arsenic has a complex biogeochemical cycle which has a significant role in pollution. Therefore, this review paper has comprehensively analysed the biogeochemical cycle of arsenic which can dictate the occurrence of arsenic pollution. Considering the toxicity and nature of arsenic, the present work has also analysed the current status of arsenic pollution around the world. It is noted that the south of Asia, West-central Africa, west of Europe and Latin America are major hot spots of arsenic pollution. Bibliometric analysis was performed by using scopus database with specific search for keywords such as arsenic pollution, health hazards to obtain the relevant data. Scopus database was searched for the period of 20 years from year 2003-2023 and total of 1839 articles were finally selected for further analysis using VOS viewer. Bibliometric analysis of arsenic pollution and its health hazards has revealed that arsenic pollution is primarily caused by anthropogenic sources and the key sources of arsenic exposure are drinking water, sea food and agricultural produces. Arsenic pollution was found to be associated with severe health hazards such as cancer and other health issues. Thus considering the severity of the issue, few sustainable remediation technologies such as adsorption using microbes, biological waste material, nanomaterial, constructed wetland, phytoremediation and microorganism bioremediation are proposed for treating arsenic pollution. These approaches are environmentally friendly and highly sustainable, thus making them suitable for the current scenario of environmental crisis.

Be2+ Causes Hypersensitivity but Mg2+ and Ca2+ Do Not─Favorable Metal Coordination Is the Key for Differential Allosteric Modulation and Binding Affinities

Although the ion selectivity of metalloproteins has been well established, selective metal antigen recognition by immunoproteins remains elusive. One such case is the recognition of the Be2+ ion against its heavier congeners, Mg2+ and Ca2+, by the human leukocyte antigen immunoprotein (HLA-DP2), leading to immunotoxicity. Integrating with our previous mechanistic study on Be2+ toxicity, herein, we have explored the basis of characteristic nontoxicity of Mg2+ and Ca2+ ions despite their in vivo abundance. The ion binding cleft of the HLA-DP2-peptide complex is composed of four acidic residues, p4D and p7E from the peptide and β26E and β69E from the protein. While the tetrahedral coordination site of the smaller Be2+ ion is located deep inside the cavity, hexa- to octa-coordination sites of Mg2+ and Ca2+ ions are located closer to the protein surface. The intrinsic high coordination number of Mg2+/Ca2+ ions induces allosteric modifications on the HLA-DP2_M2 surface, which are atypical for TCR recognition. Furthermore, the lower binding energy of larger Mg2+ and Ca2+ ions with the cavity residues can be correlated to the lower charge density and reduced covalent bonding nature as compared to those of the smaller Be2+ ion. In short, weak binding of Mg2+ and Ca2+ ions and the unfavorable allosteric surface modifications are probably the major determinants for the absence of Mg2+/Ca2+ ion-mediated hypersensitivity in humans.

Characterization of a novel ArsR regulates divergent ars operon in Ensifer adhaerens strain ST2

Microbes evolved resistance determinates for coping with arsenic toxicity are commonly regulated by a variety of transcriptional repressors (ArsRs). Ensifer adhaerens strain ST2 was previously shown tolerance to environmental organoarsenical methylarsenite (MAs(III)), which has been proposed to be a primordial antibiotic. In E. adhaerens strain ST2 chromosomal ars operon, two MAs(III) resistance genes, arsZ, encoding MAs(III) oxidase, and arsK, encoding MAs(III) efflux transporter, are controlled by a novel ArsR transcriptional repressor, EaArsR. It has two conserved cysteine pairs, Cys91-92 and Cys108-109. Electrophoretic mobility shift assays (EMSAs) demonstrate that EaArsR binds to two inverted-repeat sequences within the ars promoter between arsR and arsZ to repress ars operon transcription and that DNA binding is relieved upon binding of As(III) and MAs(III). Mutation of either Cys91 or Cys92 to serine (or both) abolished these mutants binding to the ars promoter. In contrast, both C108S and C109S mutants kept responsiveness to As(III) and MAs(III). These results suggest that cysteine pair Cys91-Cys92 and either Cys108 or Cys109 contribute to form arsenic binding site. Homology modeling of EaArsR indicates the binding site consisted of Cys91-Cys92 pair from one monomer and Cys108-Cys109 pair from the other monomer, which displays the diverse evolution of arsenic binding site in the ArsR metalloregulators.

Fluorescent Aptaswitch for Detection of Lead Ions

Detection of metal ions has essential roles in biology, food industry, and environmental sciences. In this work, we developed a Pb²⁺ detection strategy based on a fluorophore-tagged Pb²⁺-binding aptamer. The DNA aptamer changes its conformation on binding Pb²⁺, switching from an "off" state (low fluorescence) to an "on" state (high fluorescence). This method provides a quantitative readout with a detection limit of 468 nM, is highly specific to Pb²⁺ when tested against other metal ions, and is functional in complex biofluids. Such metal sensing DNA aptamers could be coupled with other biomolecules for sense-and-actuate mechanisms in biomedical and environmental applications.

Thermoresponsive Metallo-protein-based Hybrid Hydro-gels for Reversible and Highly Selective Removal of Lead(II) from Water

It is interesting to develop biomaterials for easily removing ultra-trace toxic metal ions from the environment. Herein, we have synthesized a thermoresponsive hybrid hydrogel PNIPAM-co-PbrRP by incorporating a reconstituted lead-binding...

Recent advances in bacterial biosensing and bioremediation of cadmium pollution: a mini-review

Cadmium (Cd) pollution has become a global environmental issue because Cd gets easily accumulated and translocated in the food chain, threatening human health. Considering the detrimental effects and non-biodegradability of environmental Cd, this is an urgent issue that needs to be addressed through the development of robust, cost-effective, and eco-friendly green routes for monitoring and remediating toxic levels of Cd. This article attempts to review various bacterial approaches toward biosensing and bioremediation of Cd in the environment. This review focuses on the recent development of bacterial cell-based biosensors for the detection of bioavailable Cd and the bioremediation of toxic Cd by natural or genetically-engineered bacteria. The present limitations and future perspectives of these available bacterial approaches are outlined. New trends for integrating synthetic biology and metabolic engineering into the design of bacterial biosensors and bioadsorbers are additionally highlighted.

Open Reading Frame 1 Protein of the Human Long Interspersed Nuclear Element 1 Retrotransposon Binds Multiple Equivalents of Lead

The human long interspersed nuclear element 1 (LINE1) has been implicated in numerous diseases and has been suggested to play a significant role in genetic evolution. Open reading frame 1 protein (ORF1p) is one of the two proteins encoded in this self-replicating mobile genetic element, both of which are essential for retrotransposition. The structure of the three-stranded coiled-coil domain of ORF1p was recently solved and showed the presence of tris-cysteine layers in the interior of the coiled-coil that could function as metal binding sites. Here, we demonstrate that ORF1p binds Pb(II). We designed a model peptide, GRCSL16CL23C, to mimic two of the ORF1p Cys3 layers and crystallized the peptide both as the apo-form and in the presence of Pb(II). Structural comparison of the ORF1p with apo-(GRCSL16CL23C)3 shows very similar Cys3 layers, preorganized for Pb(II) binding. We propose that exposure to heavy metals, such as lead, could influence directly the structural parameters of ORF1p and thus impact the overall LINE1 retrotransposition frequency, directly relating heavy metal exposure to genetic modification.

Temperature-Driven Metalloprotein-Based Hybrid Hydrogels for Selective and Reversible Removal of Cadmium(II) from Water

To develop biomaterials that easily and reversibly remove trace amounts of metal ions, we synthesized PNIPAM-co-CadRP, a thermally sensitive hybrid hydrogel by immobilizing a reconstituted cadmium binding peptide (CadRP) derived from the metalloregulatory protein CadR in a poly(N-isopropylacrylamide) (PNIPAM) gel network. The hybrid hydrogel retains the properties of the immobilized peptide and highly sensitively and selectively binds Cd(II) ions. The thermally sensitive properties of the hybrid hydrogel, which swells at low temperatures (<34 °C) and shrinks at high temperatures, provides a driving force sufficient to alternate the conformation of the immobilized CadRP such that the peptide captures and releases metal ions at high and low temperatures, respectively. Using this novel hybrid gel, we captured nanomolar Cd(II) from samples of environmental water in a highly efficient manner, leading to a practical and repeatedly reusable material to remediate our environment.

Fluorescence Anisotropy Reduction of An Allosteric G-Rich Oligonucleotide for Specific Silver Ion and Cysteine Detection Based on the G-Ag+-G Base Pair

Silver is a common heavy metal, and the detection of silver ion (Ag⁺) is of great importance because of its wide application and hazardous effect on the environment and human health. However, it is a great challenge to produce a large fluorescence anisotropy (FA) change for small molecules (e.g, Ag⁺). Herein, we describe a novel fluorescence anisotropy reduction approach for the sensitive and specific detection of Ag⁺. The feasibility of this method is demonstrated through screening a number of guanine-rich oligonucleotide probes. By selectively labeling the oligonucleotides with a single fluorophore tetramethylrhodamine (TMR), the reduction in FA response is associated with the conformation change from the unfolded to a hairpin-like folded structure by inducing formation of the intermolecular G-Ag⁺-G base pair, which diminishes the interaction between guanine and TMR by photoinduced electron transfer (PET). The change in FA allows the selective detection of Ag⁺ at a concentration as low as 0.5 nM with a dynamic range from 2.0 to 100 nM. The interference from the other 14 metal ions with a 100-fold even to a 1000-fold excess amount is negligible. This simple and cost-effective probe was further explored to determine cysteine (Cys) based on competing with a guanine-rich oligonucelotide for Ag⁺-binding.

Crystal structures of manganese-dependent transcriptional repressor MntR (Rv2788) from Mycobacterium tuberculosis in apo and manganese bound forms

The pathogenic Mycobacterium tuberculosis encodes two members of the DtxR family metalloregulators, IdeR and MntR. IdeR represses gene expression in response to ferrous iron, while MntR (Rv2788) functions as a manganese-dependent transcriptional repressor, which represses the expression of manganese transporter genes to maintain manganese homeostasis. Although the structural study towards IdeR is in-depth, there is no MntR structure available. Herein, we report both apo and manganese bound forms of MntR structures from M. tuberculosis. MntR has evolved into two metal ion binding sites like other DtxR proteins and for the first time, we captured the two sites fully occupied by its natural ions with one Mn²⁺ ion at the first site and two Mn²⁺ ions at the second binding site (binuclear manganese cluster). The conformation change of MntR resulting from manganese binding could prime the MntR for DNA binding, which is a conserved activation mechanism among DtxR family.

Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators

The large yybP-ykoY family of bacterial riboswitches is broadly distributed phylogenetically. Previously, these gene-regulatory RNAs were proposed to respond to Mn²⁺. X-ray crystallography revealed a binuclear cation-binding pocket. This comprises one hexacoordinate site, with six oxygen ligands, which preorganizes the second, with five oxygen and one nitrogen ligands. The relatively soft nitrogen ligand was proposed to confer affinity for Mn²⁺, but how this excludes other soft cations remained enigmatic. By subjecting representative yybP-ykoY riboswitches to diverse cations in vitro, we now find that these RNAs exhibit limited transition metal ion selectivity. Among the cations tested, Cd²⁺ and Mn²⁺ bind most tightly, and comparison of three new Cd²⁺-bound crystal structures suggests that these riboswitches achieve selectivity by enforcing heptacoordination (favored by high-spin Cd²⁺ and Mn²⁺, but otherwise uncommon) in the softer site. Remarkably, the Cd²⁺- and Mn²⁺-selective bacterial transcription factor MntR also uses heptacoordination within a binuclear site to achieve selectivity.

Lead(II) Binding in Natural and Artificial Proteins

This article describes recent attempts to understand the biological chemistry of lead using a synthetic biology approach. Lead binds to a variety of different biomolecules ranging from enzymes to regulatory and signaling proteins to bone matrix. We have focused on the interactions of this element in thiolate-rich sites that are found in metalloregulatory proteins such as Pbr, Znt, and CadC and in enzymes such as δ-aminolevulinic acid dehydratase (ALAD). In these proteins, Pb(II) is often found as a homoleptic and hemidirectic Pb(II)(SR)3- complex. Using first principles of biophysics, we have developed relatively short peptides that can associate into three-stranded coiled coils (3SCCs), in which a cysteine group is incorporated into the hydrophobic core to generate a (cysteine)3 binding site. We describe how lead may be sequestered into these sites, the characteristic spectral features may be observed for such systems and we provide crystallographic insight on metal binding. The Pb(II)(SR)3- that is revealed within these α-helical assemblies forms a trigonal pyramidal structure (having an endo orientation) with distinct conformations than are also found in natural proteins (having an exo conformation). This structural insight, combined with 207Pb NMR spectroscopy, suggests that while Pb(II) prefers hemidirected Pb(II)(SR)3- scaffolds regardless of the protein fold, the way this is achieved within α-helical systems is different than in β-sheet or loop regions of proteins. These interactions between metal coordination preference and protein structural preference undoubtedly are exploited in natural systems to allow for protein conformation changes that define function. Thus, using a design approach that separates the numerous factors that lead to stable natural proteins allows us to extract fundamental concepts on how metals behave in biological systems.

Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors

The large and increasing volume of genomic data analyzed by comparative methods provides information about transcription factors and their binding sites that, in turn, enables statistical analysis of correlations between factors and sites, uncovering mechanisms and evolution of specific protein-DNA recognition. Here we present an online tool, Prot-DNA-Korr, designed to identify and analyze crucial protein-DNA pairs of positions in a family of transcription factors. Correlations are identified by analysis of mutual information between columns of protein and DNA alignments. The algorithm reduces the effects of common phylogenetic history and of abundance of closely related proteins and binding sites. We apply it to five closely related subfamilies of the MerR family of bacterial transcription factors that regulate heavy metal resistance systems. We validate the approach using known 3D structures of MerR-family proteins in complexes with their cognate DNA binding sites and demonstrate that a significant fraction of correlated positions indeed form specific side-chain-to-base contacts. The joint distribution of amino acids and nucleotides hence may be used to predict changes of specificity for point mutations in transcription factors.

Advanced purification strategy for CueR, a cysteine containing copper(I) and DNA binding protein

Metal ion regulation is essential for living organisms. In prokaryotes metal ion dependent transcriptional factors, the so-called metalloregulatory proteins play a fundamental role in controlling the concentration of metal ions. These proteins recognize metal ions with an outstanding selectivity. A detailed understanding of their function may be exploited in potential health, environmental and analytical applications. Members of the MerR protein family sense a broad range of mostly late transition and heavy metal ions through their cysteine thiolates. The air sensitivity of latter groups makes the expression and purification of such proteins challenging. Here we describe a method for the purification of the copper-regulatory CueR protein under optimized conditions. In order to avoid protein precipitation and/or eventual aggregation and to get rid of the co-purifying Escherichia coli elongation factor, our procedure consisted of four steps supplemented by DNA digestion. Subsequent anion exchange on Sepharose FF Q 16/10, affinity chromatography on Heparin FF 16/10, second anion exchange on Source 30 Q 16/13 and gel filtration on Superdex 75 26/60 resulted in large amounts of pure CueR protein without any affinity tag. Structure and functionality tests performed with mass spectrometry, circular dichroism spectroscopy and electrophoretic gel mobility shift assays approved the success of the purification procedure.

Chromium(III) Binding Phage Screening for the Selective Adsorption of Cr(III) and Chromium Speciation

The screening of suitable sorption medium is the key for highly selective solid phase extraction (SPE) of heavy metals. Herein, we demonstrate a universal protocol for producing selective SPE adsorbent through an evolutional approach based on phage display peptide library. By choosing chromium(III) as the model target, immobilized Cr(III) resins are first prepared using Ni-NTA affinity resins for the interaction with NEB heptapeptide phage library. After three rounds of positive biopanning against target Cr(III) and negative biopanning against foreign metal species, Cr(III) binding phages with high selectivity are obtained. The binding affinity and selectivity are further assessed with ELISA. The phages bearing peptide (YKASLIT) is finally chosen and immobilized on cytopore beads for Cr(III) preconcentration. The retained Cr(III) is efficiently recovered by 0.10 mol L(-1) HNO3 and quantified with ICP-MS. By loading 4000 μL of sample solution at pH 7.0 for 2 h and stripping with 400 μL of 0.10 mol L(-1) HNO3, a linear range of 0.05-0.50 μg L(-1) is achieved along with an enrichment factor of 7.1. The limit of detection is derived to be 15 ng L(-1) (3σ, n = 7) with a RSD of 3.6% (0.25 μg L(-1), n = 7). The procedure is validated by analyzing chromium content in a certified reference material GBW08608 (simulate water). In addition, chromium speciation in real water samples is demonstrated. Cr(VI) is first converted into Cr(III), and the latter subjected to the sorption onto the Cr(III) binding phage, followed by elution and quantification of the total chromium amount, and finally speciation is achieved by difference.

An intimate link: two-component signal transduction systems and metal transport systems in bacteria

Bacteria have evolved various strategies to contend with high concentrations of environmental heavy metal ions for rapid, adaptive responses to maintain cell viability. Evidence gathered in the past two decades suggests that bacterial two-component signal transduction systems (TCSTSs) are intimately involved in monitoring cation accumulation, and can regulate the expression of related metabolic and virulence genes to elicit adaptive responses to changes in the concentration of these ions. Using examples garnered from recent studies, we summarize the cross-regulatory relationships between metal ions and TCSTSs. We present evidence of how bacterial TCSTSs modulate metal ion homeostasis and also how metal ions, in turn, function to control the activities of these signaling systems linked with bacterial survival and virulence.

Structural basis of the mercury(II)-mediated conformational switching of the dual-function transcriptional regulator MerR

The mer operon confers bacterial resistance to inorganic mercury (Hg(2+)) and organomercurials by encoding proteins involved in sensing, transport and detoxification of these cytotoxic agents. Expression of the mer operon is under tight control by the dual-function transcriptional regulator MerR. The metal-free, apo MerR binds to the mer operator/promoter region as a repressor to block transcription initiation, but is converted into an activator upon Hg(2+)-binding. To understand how MerR interacts with Hg(2+) and how Hg(2+)-binding modulates MerR function, we report here the crystal structures of apo and Hg(2+)-bound MerR from Bacillus megaterium, corresponding respectively to the repressor and activator conformation of MerR. To our knowledge, the apo-MerR structure represents the first visualization of a MerR family member in its intact and inducer-free form. And the Hg(2+)-MerR structure offers the first view of a triligated Hg(2+)-thiolate center in a metalloprotein, confirming that MerR binds Hg(2+) via trigonal planar coordination geometry. Structural comparison revealed the conformational transition of MerR is coupled to the assembly/disassembly of a buried Hg(2+) binding site, thereby providing a structural basis for the Hg(2+)-mediated functional switching of MerR. The pronounced Hg(2+)-induced repositioning of the MerR DNA-binding domains suggests a plausible mechanism for the transcriptional regulation of the mer operon.

A single serine residue determines selectivity to monovalent metal ions in metalloregulators of the MerR family

MerR metalloregulators alleviate toxicity caused by an excess of metal ions, such as copper, zinc, mercury, lead, cadmium, silver, or gold, by triggering the expression of specific efflux or detoxification systems upon metal detection. The sensor protein binds the inducer metal ion by using two conserved cysteine residues at the C-terminal metal-binding loop (MBL). Divalent metal ion sensors, such as MerR and ZntR, require a third cysteine residue, located at the beginning of the dimerization (α5) helix, for metal coordination, while monovalent metal ion sensors, such as CueR and GolS, have a serine residue at this position. This serine residue was proposed to provide hydrophobic and steric restrictions to privilege the binding of monovalent metal ions. Here we show that the presence of alanine at this position does not modify the activation pattern of monovalent metal sensors. In contrast, GolS or CueR mutant sensors with a substitution of cysteine for the serine residue respond to monovalent metal ions or Hg(II) with high sensitivities. Furthermore, in a mutant deleted of the Zn(II) exporter ZntA, they also trigger the expression of their target genes in response to either Zn(II), Cd(II), Pb(II), or Co(II).

IMPORTANCE

Specificity in a stressor's recognition is essential for mounting an appropriate response. MerR metalloregulators trigger the expression of specific resistance systems upon detection of heavy metal ions. Two groups of these metalloregulators can be distinguished, recognizing either +1 or +2 metal ions, depending on the presence of a conserved serine in the former or a cysteine in the latter. Here we demonstrate that the serine residue in monovalent metal ion sensors excludes divalent metal ion detection, as its replacement by cysteine renders a pan-metal ion sensor. Our results indicate that the spectrum of signals detected by these sensors is determined not only by the metal-binding ligand availability but also by the metal-binding cavity flexibility.

The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia

BACKGROUND

Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb(2+), Al(+3), SeO2, Cu(2+), AsO4, and Zn(2+). With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison.

RESULTS

Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia.

CONCLUSIONS

Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.

Structural metal sites in nonclassical zinc finger proteins involved in transcriptional and translational regulation

Zinc finger (ZF) proteins are a large family of metalloproteins that utilize zinc for structural purposes. Zinc coordinates to a combination of cysteine thiol and histidine imidazole residues within the ZF polypeptide sequence resulting in a folded and functional protein. Initially, a single class of ZFs were identified. These ZFs, now referred to as the "classical" ZFs, utilize a Cys2His2 (CCHH) ligand set to bind zinc. Upon Zn coordination, the classical ZFs fold into a structure made up of an α helix and an antiparallel β sheet. When folded, classical ZFs recognize and bind to specific DNA targets and function as transcription factors. With the advent of genome sequencing and proteomics, many additional classes of ZFs were identified based upon their primary amino acid sequences. At least 13 additional classes of ZFs are known, and collectively these "nonclassical" ZFs differ in the ligand set involved in Zn(II) coordination, the organization of the ligands within the polypeptide sequence and the macromolecular targets. Some nonclassical ZFs are DNA binding "transcription factors", while others are involved in RNA regulation and protein recognition. Much less is known about these nonclassical ZFs with regards to the roles of metal coordination in fold and function. This Account focuses on our laboratory's efforts to characterize two families of "nonclassical" ZFs: the Cys3His (or CCCH) ZF family and the Cys2His2Cys (or CCHHC) ZF family. Our work on the CCCH ZF family has focused on the protein Tristetraprolin (TTP), which is a key protein in regulating inflammation. TTP contains two CCCH domains that were proposed to be ZFs based upon their sequence. We have shown that while this protein can coordinate Zn(II) at the CCCH sites, it can also coordinate Fe(II) and Fe(III). Moreover, the zinc and iron bound forms of TTP are equally adept at discriminating between RNA targets, which we have demonstrated via a fluorescence anisotropy based approach. Thus, CCCH type ZFs appear to be promiscuous with respect to metal preference and a role for iron coordination in CCCH ZF function is proposed. The CCHHC family of ZFs is a small family of nonclassical ZFs that are essential for the development of the central nervous system. There are three ZFs in this family: neural zinc finger factor-1 (NZF-1), myelin transcription factor-1 (MyT1), and suppressor of tumorgenicity 18 (ST18). All three proteins contain multiple clusters of "CCHHC" domains, which are all predicted to be Zn binding domains. We have focused on a tandem-CCHHC domain construct of NZF-1, which recognizes β-RARE DNA, and we have identified key residues required for DNA recognition. Unlike classical ZFs, for which a few conserved residues are required for DNA recognition, the CCHHC class of ZFs utilize a few nonconserved residues to drive DNA recognition leading us to propose a new paradigm for ZF/DNA binding.

Efficient preparation and metal specificity of the regulatory protein TroR from the human pathogen Treponema pallidum

TroR is a putative metal-dependent regulatory protein that has been linked to the virulence of the human pathogen Treponema pallidum. It shares high homology with the well-known iron-dependent regulatory protein DtxR from Corynebacterium diphtheriae, as well as the manganese-dependent MntR from Bacillus subtilis. However, it has been uncertain whether manganese or zinc is the natural cofactor of TroR to date. Herein, we established an efficient method named "double-fusion tagging" to obtain soluble TroR for the first time. A series of studies, including ICP, CD, fluorescence, ITC, and electrophoresis mobility shift assay (EMSA), were performed to resolve the discrepancies in its metal-binding specificity. In addition, bioinformatic analysis as well as mutation studies were carried out to find the genetic relationships of TroR with its homology proteins. In conclusion, our findings indicate that TroR is a manganese-dependent rather than a zinc-dependent regulatory protein.

DNA as sensors and imaging agents for metal ions

Increasing interest in detecting metal ions in many chemical and biomedical fields has created demands for developing sensors and imaging agents for metal ions with high sensitivity and selectivity. This review covers recent progress in DNA-based sensors and imaging agents for metal ions. Through both combinatorial selection and rational design, a number of metal-ion-dependent DNAzymes and metal-ion-binding DNA structures that can selectively recognize specific metal ions have been obtained. By attachment of these DNA molecules with signal reporters such as fluorophores, chromophores, electrochemical tags, and Raman tags, a number of DNA-based sensors for both diamagnetic and paramagnetic metal ions have been developed for fluorescent, colorimetric, electrochemical, and surface Raman detection. These sensors are highly sensitive (with a detection limit down to 11 ppt) and selective (with selectivity up to millions-fold) toward specific metal ions. In addition, through further development to simplify the operation, such as the use of "dipstick tests", portable fluorometers, computer-readable disks, and widely available glucose meters, these sensors have been applied for on-site and real-time environmental monitoring and point-of-care medical diagnostics. The use of these sensors for in situ cellular imaging has also been reported. The generality of the combinatorial selection to obtain DNAzymes for almost any metal ion in any oxidation state and the ease of modification of the DNA with different signal reporters make DNA an emerging and promising class of molecules for metal-ion sensing and imaging in many fields of applications.

Lead resistance in micro-organisms

Lead (Pb) is an element present in the environment that negatively affects all living organisms. To diminish its high toxicity, micro-organisms have developed several mechanisms that allow them to survive exposure to Pb(II). The main mechanisms of lead resistance involve adsorption by extracellular polysaccharides, cell exclusion, sequestration as insoluble phosphates, and ion efflux to the cell exterior. This review describes the various lead resistance mechanisms, and the regulation of their expression by lead binding regulatory proteins. Special attention is given to the Pbr system from Cupriavidus metallidurans CH34, which involves a unique mechanism combining efflux and lead precipitation.

Single-molecule dynamics and mechanisms of metalloregulators and metallochaperones

Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interface of chemistry and biology. This Current Topic reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein-DNA and protein-protein interactions offer efficient pathways via which MerR-family metalloregulators and copper chaperones can fulfill their functions. This work also summarizes other related single-molecule studies of bioinorganic systems and provides an outlook toward single-molecule imaging of metalloprotein functions in living cells.

Copper efflux is induced during anaerobic amino acid limitation in Escherichia coli to protect iron-sulfur cluster enzymes and biogenesis

Adaptation to changing environments is essential to bacterial physiology. Here we report a unique role of the copper homeostasis system in adapting Escherichia coli to its host-relevant environment of anaerobiosis coupled with amino acid limitation. We found that expression of the copper/silver efflux pump CusCFBA was significantly upregulated during anaerobic amino acid limitation in E. coli without the supplement of exogenous copper. Inductively coupled plasma mass spectrometry analysis of the total intracellular copper content combined with transcriptional assay of the P(cusC)-lacZ reporter in the presence of specific Cu(I) chelators indicated that anaerobic amino acid limitation led to the accumulation of free Cu(I) in the periplasmic space of E. coli, resulting in Cu(I) toxicity. Cells lacking cusCFBA and another copper transporter, copA, under this condition displayed growth defects and reduced ATP production during fumarate respiration. Ectopic expression of the Fe-S cluster enzyme fumarate reductase (Frd), or supplementation with amino acids whose biosynthesis involves Fe-S cluster enzymes, rescued the poor growth of ΔcusC cells. Yet, Cu(I) treatment did not impair the Frd activity in vitro. Further studies revealed that the alternative Fe-S cluster biogenesis system Suf was induced during the anaerobic amino acid limitation, and ΔcusC enhanced this upregulation, indicating the impairment of the Fe-S cluster assembly machinery and the increased Fe-S cluster demands under this condition. Taken together, we conclude that the copper efflux system CusCFBA is induced during anaerobic amino acid limitation to protect Fe-S cluster enzymes and biogenesis from the endogenously originated Cu(I) toxicity, thus facilitating the physiological adaptation of E. coli.

Expression of arsenic regulatory protein in Escherichia coli for selective accumulation of methylated arsenic species

ArsR is a metalloregulatory protein with high selectivity and affinity toward arsenic. We hereby report the expression of ArsR in Escherichia coli by cell engineering, which significantly enhances the adsorption/accumulation capacity of methylated arsenic species. The ArsR-expressed E. coli cells (denoted as E. coli-ArsR) give rise to 5.6-fold and 3.4-fold improvements on the adsorption/accumulation capacity for monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA), with respect to native E. coli cells. The uptake of MMA and DMA by the E. coli-ArsR is a fast process fitting Langmuir adsorption model. It is interesting to note that the accumulation of methylated arsenic is virtually not affected by the presence of competing heavy-metal species, at least 10 times of Cd(II) and Pb(II) are tolerated for the adsorption of 1 mg L(-1) methylated arsenic. In addition, an ionic strength of up to 2 g L(-1) Na+ poses no obvious effect on the sorption of 1 mg L(-1) MMA and DMA. Furthermore, the accumulation of MMA and DMA is less sensitive to the variation of pH value, with respect to the blank control cells. Consequently, 82.4% of MMA and 96.3% of DMA at a concentration of 50 μg L(-1) could be readily removed from aqueous medium by 12 g L(-1) of E. coli-ArsR . This illustrates a great potential for the E. coli-ArsR for selective remediation of methylated arsenic species in waters, even in the presence of a high concentration of salts.

An invasive DNA approach toward a general method for portable quantification of metal ions using a personal glucose meter

We report herein a general methodology for metal ion detection using low-cost, simple, and widely accessible personal glucose meters through an invasive DNA approach.

Roles of the A and C sites in the manganese-specific activation of MntR

The manganese transport regulator (MntR) represses the expression of genes involved in manganese uptake in Bacillus subtilis. It selectively responds to Mn(2+) and Cd(2+) over other divalent metal cations, including Fe(2+), Co(2+), and Zn(2+). Previous work has shown that MntR forms binuclear complexes with Mn(2+) or Cd(2+) at two binding sites, labeled A and C, that are separated by 4.4 Å. Zinc activates MntR poorly and binds only to the A site, forming a mononuclear complex. The difference in metal binding stoichiometry suggested a mechanism for selectivity in MntR. Larger metal cations are strongly activating because they can form the binuclear complex, while smaller metal ions cannot bind with the geometry needed to fully occupy both metal binding sites. To investigate this hypothesis, structures of MntR in complex with two other noncognate metal ions, Fe(2+) and Co(2+), have been determined. Each metal forms a mononuclear complex with MntR with the metal ion bound in the A site, supporting the conclusions drawn from the Zn(2+) complex. Additionally, we investigated two site-specific mutants of MntR, E11K and H77A, that contain substitutions of metal binding residues in the A site. While metal binding in each mutant is significantly altered relative to that of wild-type MntR, both mutants retain activity and selectivity for Mn(2+) in vitro and in vivo. That observation, coupled with previous studies, suggests that the A and C sites both contribute to the selectivity of MntR.

The zinc-responsive regulon of Neisseria meningitidis comprises 17 genes under control of a Zur element

Zinc is a bivalent cation essential for bacterial growth and metabolism. The human pathogen Neisseria meningitidis expresses a homologue of the Zinc uptake regulator Zur, which has been postulated to repress the putative zinc uptake protein ZnuD. In this study, we elucidated the transcriptome of meningococci in response to zinc by microarrays and quantitative real-time PCR (qRT-PCR). We identified 15 genes that were repressed and two genes that were activated upon zinc addition. All transcription units (genes and operons) harbored a putative Zur binding motif in their promoter regions. A meningococcal Zur binding consensus motif (Zur box) was deduced in silico, which harbors a conserved central palindrome consisting of hexameric inverted repeats separated by three nucleotides (TGTTATDNHATAACA). In vitro binding of recombinant meningococcal Zur to this Zur box was shown for the first time using electrophoretic mobility shift assays. Zur binding to DNA depended specifically on the presence of zinc and was sensitive to mutations in the palindromic sequence. The Zur regulon among genes of unknown function comprised genes involved in zinc uptake, tRNA modification, and ribosomal assembly. In summary, this is the first study of the transcriptional response to zinc in meningococci.

Direct detection of adenosine in undiluted serum using a luminescent aptamer sensor attached to a terbium complex

Aptamers, single-stranded nucleic acids that can selectively bind to various target molecules, have been widely used for constructing biosensors. A major challenge in this field, however, is direct sensing of analytes in complex biological media such as undiluted serum. While progress has been made in developing an inhomogeneous assay by using a preseparation step to wash away the interferences within serum, a facile strategy for direct detection of targets in homogeneous unprocessed serum is highly desired. We herein report a turn-on luminescent aptamer biosensor for the direct detection of adenosine in undiluted and unprocessed serum, by taking advantage of a terbium chelate complex with long luminescence lifetime to achieve time-resolved detection. The sensor exhibits a detection limit of 60 μM adenosine while marinating excellent selectivity that is comparable to those in buffer. The approach demonstrated here can be applied for direct detection and quantification of a broad range of analytes in biological media by using other aptamers.

Regulation of MntH by a dual Mn(II)- and Fe(II)-dependent transcriptional repressor (DR2539) in Deinococcus radiodurans

The high intracellular Mn/Fe ratio observed within the bacteria Deinococcus radiodurans may contribute to its remarkable resistance to environmental stresses. We isolated DR2539, a novel regulator of intracellular Mn/Fe homeostasis in D. radiodurans. Electrophoretic gel mobility shift assays (EMSAs) revealed that DR2539 binds specifically to the promoter of the manganese acquisition transporter (MntH) gene, and that DR0865, the only Fur homologue in D. radiodurans, cannot bind to the promoter of mntH, but it can bind to the promoter of another manganese acquisition transporter, MntABC. β-galactosidase expression analysis indicated that DR2539 acts as a manganese- and iron-dependent transcriptional repressor. Further sequence alignment analysis revealed that DR2539 has evolved some special characteristics. Site-directed mutagenesis suggested that His98 plays an important role in the activities of DR2539, and further protein-DNA binding activity assays showed that the activity of H98Y mutants decreased dramatically relative to wild type DR2539. Our study suggests that D. radiodurans has evolved a very efficient manganese regulation mechanism that involves its high intracellular Mn/Fe ratio and permits resistance to extreme conditions.

Portable and quantitative detection of protein biomarkers and small molecular toxins using antibodies and ubiquitous personal glucose meters

Developing portable and low-cost methods for quantitative detection of large protein biomarkers and small molecular toxins can play a significant role in controlling and preventing diseases or toxins outbreaks. Despite years of research, most current methods still require laboratory-based or customized devices that are not widely available to the general public for quantitative analysis. We have previously demonstrated the use of personal glucose meters (PGMs) and functional DNAs for the detection of many nonglucose targets. However, the range of targets detectable by functional DNAs is limited at the current stage. To expand the range of targets that can be detected by PGMs, we report here the use of antibodies in combination with sandwich and competitive assays for quantitative detection of protein biomarkers (PSA, with a detection limit of 0.4 ng/mL) and small molecular toxins (Ochratoxin A, with a detection limit of 6.8 ng/mL), respectively. In both assay methods, with invertase conjugates as the link, quantitative detection is achieved via the dependence between the concentrations of the targets in the sample and the glucose measured by PGMs. Given the wide availability of antibodies for numerous targets, the methods demonstrated here can expand the range of target detection by PGMs significantly.

Label-free catalytic and molecular beacon containing an abasic site for sensitive fluorescent detection of small inorganic and organic molecules

In this work, two methods with complementary features, catalytic and molecular beacon (CAMB) and label-free fluorescent sensors using an abasic site, have been combined into new label-free CAMB sensors that possess advantages of each method. The label-free method using a dSpacer-containing molecular beacon makes CAMB more cost-effective and less interfering with the catalytic activity, while CAMB allows the label-free method to use true catalytic turnovers for signal amplifications, resulting in a new label-free CAMB sensor for Pb(2+) ion, with a detection limit of 3.8 nM while maintaining the same selectivity. Furthermore, by using CAMB to overcome the label-free method's limitation of requiring excess enzyme strands, a new label-free CAMB sensor using aptazyme is also designed to detect adenosine down to 1.4 μM, with excellent selectivity over other nucleosides.